Nontuberculous mycobacteria (NTM), including Mycobacterium abscessus (MAB) and species in the Mycobacterium avium complex (MAC), are opportunistic pathogens that cause human lung disease. Epidemiological studies show increasing prevalence of pulmonary NTM infections, especially in individuals with cystic fibrosis (CF) and adults over 50 with non-CF bronchiectasis. Only 40-50% of patients with positive respiratory NTM cultures progress to active lung disease. Therefore, the clinical decision to treat is difficult given that NTM are resistant to most classes of antibiotics, and treatment lasts a year or more with varying success and drug toxicities. On the pathogen side, very little is known about the genetic variability of the isolate population, and disease transmission is poorly understood. In MAB, recent genomic studies suggest the possibility of person-to-person transmission within CF clinics raising significant public health concerns. In MAC, which comprise the majority of NTM cases, there have been no population genomics studies to date. The work proposed here will provide a foundational understanding of the genetic epidemiology of MAB and MAC by analyzing whole genome sequence (WGS) data of a clinical isolate cohort from an ongoing study in CF patients (n=600) and also generating a comparable WGS dataset for isolates derived from non-CF patients (n=300). Genomic polymorphisms will be evaluated, and strain subtypes within clinical MAB and MAC populations will be identified for the combined isolate cohort (CF and non-CF). Then, the strain subtypes will be statistically associated with patient clinical variables including age, gender, lung function, co-infection with Pseudomonas aeruginosa, CF diagnosis and active lung disease to test the hypothesis that certain genetic subtypes preferentially infect patient subpopulations. In a more detailed analysis, CF patients with NTM will be stratified by infection status (transient, indolent or active lung disease) based on the American Thoracic Society's criteria for disease, to test the hypothesis that one or more strain subtypes are predictive of individuals who progress to active NTM lung disease. Results from this study will be significant because they will provide a mechanistic basis for improved diagnosis and treatment of emerging pathogens in high-risk patient populations. The proposed research strategy and comprehensive career development training plan build on the PI's previous training in molecular and computational biology in order to gain expertise in human epidemiology, statistical genetics and clinical outcomes research. The PI will be co-mentored by an established genetic epidemiologist and a clinical expert in CF and NTM diseases in the unparalleled research environment at National Jewish Health (NJH), the nation's leading respiratory hospital. The PI is uniquely positioned to become a successful, independent investigator in biomedical research due to the established, integrated clinical and research infrastructure at NJH, a national referral center for NTM, CF and other pulmonary diseases.